[ccp4bb] 100% Rmerge in high resolution shell
Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com
Re: [ccp4bb] translational pseudo symmetry
Hi Eleanor, I checked P43212 and P41212 by changing the header of mtz file and running refmac for the same PDB input. P43212 is a better match than P41212. Sincerely, Dan From: CCP4 bulletin board on behalf of Eleanor Dodson Sent: Monday, November 18, 2013 8:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] translational pseudo symmetry I guess you have checked that P43212 is a better match than P41212? (And that you are running REFMAC against an mtz file with the same symmetry as the input PDB - you may need to change the SG in the mtz header by hand. mtzutils hklin P41212.mtz hklout P43212.mtz symm P43212 end Or vice versa.. Sorry - THIS IS CRAZY but there you are.. Re the pseudo translation -Randy summs up the situation very clearly. I would build my model by hand actually but I am sure PHASER does itwell too! Something I dont understand but maybe it is to do with your patterson sampling. Peak 3 is a consequence of Pk 1 and Pk2 - Pk 5 is the consequence of Pk 1 and Pk4 but the peak heights dont exactly fit.. Eleanor On 18 November 2013 10:19, Randy Read wrote: > Dear Dan, > > First, you don't want to reprocess in the smaller cell. What xtriage is > saying is that, if *and only if* the translation detected in the Patterson > map were an exact crystallographic translation, then you would get the > smaller cell. However, in order for that to be a plausible hypothesis, the > Patterson peaks would have to be near to 100% of the origin peak. > > You actually seem to have a very interesting case, where the Patterson peaks > are related by multiples of approximately the same translation. If you take > a translation of 1/2,1/2,1/6 and multiply it by 1, 2 and 3, you get > something close to the three biggest peaks in your Patterson (taking account > of lattice translations), and these are related by the Patterson inversion > centre to what you get if you multiply by 4 and 5. So the six molecules > should be related to each other by something close to a repeated translation > of 1/2,1/2,1/6. (You should check this in the solution that you already > have.) If this were exact, you would have a smaller cell, but it's not > exact, and one way in which it is not exact is that the translations along z > are not exactly multiples of 1/6. > > This is reminiscent of a structure that we recently collaborated with > Mariusz Jaskolski and Zbyszek Dauter to solve (paper accepted for > publication in Acta D). In that case, there are seven translations of > approximately 0,0,1/7. The difficulty with cases like this is figuring out > how to break the exact symmetry. Any solution that has approximately the > right translations will basically fit the data, but you need to find the > right combination of deviations from the exact symmetry to get an optimal > answer. If you get the wrong deviations from exact symmetry, the refinement > will stall, and this may be the problem that you're facing. > > You can deal with problems like this in Phaser by using the TNCS NMOL 6 > command (to say that there are 6 copies related by repeated applications of > the same translation). You should tell Phaser to use the 1/2,1/2,0.174 > vector (TNCS TRA VECTOR 0.5 0.5 0.174), and hopefully this will break the > symmetry in a way that subsequent rigid-body refinement can deal with. I'm > happy to give you more advice on this, off-line, because this kind of case > isn't something that we've figured out how to deal with automatically yet. > The optimal approach probably involves getting a deeper understanding of > commensurate modulation, which is another way of thinking about > pseudo-translations. > > Best wishes, > > Randy Read > > On 18 Nov 2013, at 09:19, #CHEN DAN# wrote: > > Dear experts, > > I am working on one dataset (2.5A) which was processed using space group > P43212 ( 107.9, 107.9, 313.7; 90, 90, 90). > After running MR with 6 molecules in ASU and one round of refmac, the R > factors are high (38%/45%). > I ran phenix.xtriage and found that translational pseudo symmetry is likely > present. It suggested that the space group is I4122 with the unit cell about > 1/3 smaller (I paste the patterson analyses below). > I tried to reprocess the data to get the suggested space group and unit cell > using HKL2000. But the index always gives a long c axis about 313A. > Could you provide any suggestions on how to proceed? > > Patterson analyses > -- > > Largest Patterson peak with length larger than 15 Angstrom > > Frac. coord.:0.5000.5000.174 > Distance to origin : 93.757 > Height (origin=100) : 55.763 > p_value(height) :3.018e-05 > > >The reported p_value has the following meaning: > The probability that a peak of the specified height > or larger is found in a Patterson function of a > macro molecule that does not have any translational > pseudo symmetry is equal to 3.018e-05. > p_values
Re: [ccp4bb] distinguish ligand binding sites within a protein
Hi Wei: Based on the structure, you can calculate the binding surface between the protein and the ligand. Maybe the two binding pockets will give you two different numbers. And the larger one usually can have the higher binding affinity. You also can analyse how the ligand interacts with the protein though hydrophobic or electrostatic interaction , etc? the last, you may also compare the b factors of the ligand or the protein binding pocket regions after you refining the structure. These things may give you some hints about which binding site is more strong. Dee Date: Mon, 18 Nov 2013 22:45:58 -0500 From: wei.shi...@gmail.com Subject: Re: [ccp4bb] distinguish ligand binding sites within a protein To: CCP4BB@JISCMAIL.AC.UK Thank you so much for the suggestions, Tomas! Yes, my ligand is a small molecule. I have the crystal structure of the ligands bound to the protein, do I still need to computationally dock the ligand to the two pockets, can I calculate the parameters of binding directly using the crystal structure? Best, Wei On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas wrote: Dear Wei Shi, is your ligand a small molecule? If it is a small molecule, I would try to computationally dock the small molecule to two pockets separately using AutoDock, and look at the estimated free energies of binding. Best wishes, Tomas On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi wrote: > Hi all, > I got the crystal structure of a transcription factor, and every monomer > binds two molecules of the same ligand in different binding pockets. And I > also did the ITC experiment, titrating the ligand into the protein, and got > a U-shaped curve. The binding affinity for the first binding site is higher > than the second binding site. > I am wondering whether I could computationally determine from the > protein-ligand complex structure that which binding site has higher affinity > for the ligand and correlate the binding sites with the parameters I got > from ITC experiment. > Thank you so much! > > Best, > Wei
Re: [ccp4bb] distinguish ligand binding sites within a protein
Thank you so much for the suggestions, Tomas! Yes, my ligand is a small molecule. I have the crystal structure of the ligands bound to the protein, do I still need to computationally dock the ligand to the two pockets, can I calculate the parameters of binding directly using the crystal structure? Best, Wei On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas < tomas.malinaus...@gmail.com> wrote: > Dear Wei Shi, > is your ligand a small molecule? If it is a small molecule, I would > try to computationally dock the small molecule to two pockets > separately using AutoDock, and look at the estimated free energies of > binding. > Best wishes, > Tomas > > On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi wrote: > > Hi all, > > I got the crystal structure of a transcription factor, and every monomer > > binds two molecules of the same ligand in different binding pockets. And > I > > also did the ITC experiment, titrating the ligand into the protein, and > got > > a U-shaped curve. The binding affinity for the first binding site is > higher > > than the second binding site. > > I am wondering whether I could computationally determine from the > > protein-ligand complex structure that which binding site has higher > affinity > > for the ligand and correlate the binding sites with the parameters I got > > from ITC experiment. > > Thank you so much! > > > > Best, > > Wei >
Re: [ccp4bb] distinguish ligand binding sites within a protein
Dear Wei Shi, is your ligand a small molecule? If it is a small molecule, I would try to computationally dock the small molecule to two pockets separately using AutoDock, and look at the estimated free energies of binding. Best wishes, Tomas On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi wrote: > Hi all, > I got the crystal structure of a transcription factor, and every monomer > binds two molecules of the same ligand in different binding pockets. And I > also did the ITC experiment, titrating the ligand into the protein, and got > a U-shaped curve. The binding affinity for the first binding site is higher > than the second binding site. > I am wondering whether I could computationally determine from the > protein-ligand complex structure that which binding site has higher affinity > for the ligand and correlate the binding sites with the parameters I got > from ITC experiment. > Thank you so much! > > Best, > Wei
[ccp4bb] distinguish ligand binding sites within a protein
Hi all, I got the crystal structure of a transcription factor, and every monomer binds two molecules of the same ligand in different binding pockets. And I also did the ITC experiment, titrating the ligand into the protein, and got a U-shaped curve. The binding affinity for the first binding site is higher than the second binding site. I am wondering whether I could computationally determine from the protein-ligand complex structure that which binding site has higher affinity for the ligand and correlate the binding sites with the parameters I got from ITC experiment. Thank you so much! Best, Wei
Re: [ccp4bb] Fix cell dimensions
Hi Niu - In HKL2000, you should first get an indexing solution with the 40 A axis, as you have done previously. Then go to the tab of the GUI labeled "Macros". In the bottom row, "Immediate Execution", you enter the following: unit cell a b c alpha beta gamma where you replace the words after "unit cell" with the desired unit cell dimensions, including your 20 A axis. (Make sure you use exactly half of the previous cell dimension.) Then hit "Run Macro". If it works correctly, you should see every other predicted spot disappear in your XdisplayF window. Now look to see if those predicted spots should have been removed or not! Use the zoom window to help with this. You should be able to refine the new cell parameters normally. Hope that helps, Matt On 11/18/13 5:03 PM, Niu Tou wrote: Dear Andrew, As previously I posted a MR case which has a significant 95% off origin peak, some experts suggested to reprocess the data with cutting one axis to half, from 40A to 20A. I tried HKL2000 and XDS, none of them is willing to give a solution with 20A, even I specify it in XDS script. So I wonder is there any way to force this work to be done. Thanks! Best, Niu On Mon, Nov 18, 2013 at 4:56 PM, Andrew Leslie mailto:and...@mrc-lmb.cam.ac.uk>> wrote: Dear Niu, It depends on which part of processing you are referring to, i.e. the indexing step or the integration step. In MOSFLM there is no way to enforce cell dimensions during indexing, but providing there is an indexing solution that has cell dimensions close to the ones you want, you can enforce a (slightly) different set of cell dimensions during the integration step. Normally other refined parameters will ensure that you still get a good prediction of spot positions. I suspect that this can be done in other programs too. Without knowing why you want to do this, I cannot comment on whether this is the best procedure to follow. Best wishes, Andrew On 18 Nov 2013, at 21:48, Niu Tou mailto:niutou2...@gmail.com>> wrote: > Dear All, > > Does any one know how to strictly fix the cell dimensions during data processing? In HKL2000 there is only a keyword to define the longest vector. In XDS there is a option to input cell parameters, but sometimes the program would not follow the input values > and switch back to the one it thinks best. Any suggestions will be appreciated. Thanks! > > Best, > Niu -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] Fix cell dimensions
Dear Niu, OK, I did not connect this with your earlier Email. If it is simply a case of halving one of the cell dimensions, this can be done with iMosflm by editing the cell dimensions that come from the indexing step. This will not affect the positions of the predictions, but only every second spot will be predicted along the cell edge that has been halved. It should be perfectly possible to carry out the integration this way. I would be surprised if it wasn't possible to do this with other programs. Best wishes, Andrew On 18 Nov 2013, at 22:03, Niu Tou wrote: > Dear Andrew, > > As previously I posted a MR case which has a significant 95% off origin peak, > some experts suggested to reprocess the data with cutting one axis to half, > from 40A to 20A. I tried HKL2000 and XDS, none of them is willing to give a > solution with 20A, even I specify it in XDS script. So I wonder is there any > way to force this work to be done. Thanks! > > Best, > Niu > > > On Mon, Nov 18, 2013 at 4:56 PM, Andrew Leslie > wrote: > Dear Niu, > > It depends on which part of processing you are referring to, > i.e. the indexing step or the integration step. In MOSFLM there is no way to > enforce cell dimensions during indexing, but providing there is an indexing > solution that has cell dimensions close to the ones you want, you can enforce > a (slightly) different set of cell dimensions during the integration step. > Normally other refined parameters will ensure that you still get a good > prediction of spot positions. > > I suspect that this can be done in other programs too. > > Without knowing why you want to do this, I cannot comment on whether this is > the best procedure to follow. > > Best wishes, > > Andrew > > > > On 18 Nov 2013, at 21:48, Niu Tou wrote: > > > Dear All, > > > > Does any one know how to strictly fix the cell dimensions during data > > processing? In HKL2000 there is only a keyword to define the longest > > vector. In XDS there is a option to input cell parameters, but sometimes > > the program would not follow the input values > > and switch back to the one it thinks best. Any suggestions will be > > appreciated. Thanks! > > > > Best, > > Niu > >
Re: [ccp4bb] Fix cell dimensions
Dear Niu, It depends on which part of processing you are referring to, i.e. the indexing step or the integration step. In MOSFLM there is no way to enforce cell dimensions during indexing, but providing there is an indexing solution that has cell dimensions close to the ones you want, you can enforce a (slightly) different set of cell dimensions during the integration step. Normally other refined parameters will ensure that you still get a good prediction of spot positions. I suspect that this can be done in other programs too. Without knowing why you want to do this, I cannot comment on whether this is the best procedure to follow. Best wishes, Andrew On 18 Nov 2013, at 21:48, Niu Tou wrote: > Dear All, > > Does any one know how to strictly fix the cell dimensions during data > processing? In HKL2000 there is only a keyword to define the longest vector. > In XDS there is a option to input cell parameters, but sometimes the program > would not follow the input values > and switch back to the one it thinks best. Any suggestions will be > appreciated. Thanks! > > Best, > Niu
Re: [ccp4bb] Fix cell dimensions
Dear Andrew, As previously I posted a MR case which has a significant 95% off origin peak, some experts suggested to reprocess the data with cutting one axis to half, from 40A to 20A. I tried HKL2000 and XDS, none of them is willing to give a solution with 20A, even I specify it in XDS script. So I wonder is there any way to force this work to be done. Thanks! Best, Niu On Mon, Nov 18, 2013 at 4:56 PM, Andrew Leslie wrote: > Dear Niu, > > It depends on which part of processing you are referring > to, i.e. the indexing step or the integration step. In MOSFLM there is no > way to enforce cell dimensions during indexing, but providing there is an > indexing solution that has cell dimensions close to the ones you want, you > can enforce a (slightly) different set of cell dimensions during the > integration step. Normally other refined parameters will ensure that you > still get a good prediction of spot positions. > > I suspect that this can be done in other programs too. > > Without knowing why you want to do this, I cannot comment on whether this > is the best procedure to follow. > > Best wishes, > > Andrew > > > > On 18 Nov 2013, at 21:48, Niu Tou wrote: > > > Dear All, > > > > Does any one know how to strictly fix the cell dimensions during data > processing? In HKL2000 there is only a keyword to define the longest > vector. In XDS there is a option to input cell parameters, but sometimes > the program would not follow the input values > > and switch back to the one it thinks best. Any suggestions will be > appreciated. Thanks! > > > > Best, > > Niu > >
[ccp4bb] Fix cell dimensions
Dear All, Does any one know how to strictly fix the cell dimensions during data processing? In HKL2000 there is only a keyword to define the longest vector. In XDS there is a option to input cell parameters, but sometimes the program would not follow the input values and switch back to the one it thinks best. Any suggestions will be appreciated. Thanks! Best, Niu
[ccp4bb] Fourier transforms
http://nautil.us/blog/the-math-trick-behind-mp3s-jpegs-and-homer-simpsons-face The Math Trick Behind MP3s, JPEGs, and Homer Simpson's Face Posted By Aatish Bhatia on Nov 06, 2013 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] sitcom
Dear all, i am trying to compare a set of solutions from shelxd against the correct solution and not against the generated “unique set" with sitcom my input file looks like this: unit_cell XXX space_group XXX read_sol SOLUTION 1.0 sites.pdb 18 read_set LIST 0.1 try1_fa.lst 100 18 now i tried to add the restrain_comp keyword but i can’t get it to work. thank you very much for your help, Tobias
[ccp4bb] AW: [ccp4bb] SELF-ROTATION FUNCTION FROM MOLREP
Dear Monica, strong 222 rotational symmetry plus translational symmetry would give 8 molecules in the unit cell. (4 in the a.u. in P2x and 2 in case of P2x2x2x). (test ALL options!). Do you have models for both the ligand binding domain, or only for the DNA binding domain? You have to search for the domains with separate models, not as a single model with the complete protein since the relative orientation of the domains may differ. I would just run MR jobs for 1, 2 and 3 molecules in the a.u. and for full-length and truncated models and see which one gives best results. If you make a script for it, it is very little work. Good luck! Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Monica Mittal Gesendet: Montag, 18. November 2013 14:37 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] SELF-ROTATION FUNCTION FROM MOLREP Dear CCP4 Users, In Phenix.xtriage and phaser, the analyses of the Patterson function reveals a significant off-origin peak that is 23.25 % of the origin peak, indicating pseudo translational symmetry at frac. cord. vector 0.0000.5000.022 . It did not indicate any twinng. Data is good with resolution upto 2.8A. The cell dimension in P21 SG is 57.877, 63.321, 108.028, 90, 89.987, 90 and in P222 SG is 57.805, 63.266, 108.053, 90, 90, 90. We can say cell dimension align well in in P21 and P222 SG. For MR template, about 75% of domain1, we have solved in our lab and remaining 25% is available from pdb with 30% sequence identity. It is a transcription factor with ligand bindng domain and DNA binding domain. I tried finding MR solution but does not gave satisfaction result. The Rwork and Rfree stalls around 47% and 53% respectively. Is there any possiblity to guess the no of molecules present in ASU from self-rotation function? If we can then we will be sure of whether it is full length of truncated one. Thank you Monica On 11/18/13, Eleanor Dodson wrote: > First Q - how good is your data - is there no possibility of twinning > or any other distraction? > > Second Q - To compare those results properly we need to know how the > P2 and the P222 cell align - are the cell dimensions more or less the > same? > > But the 2 plots you attach (and the list above) show both very strong > 222 symmetry so the most likely assumption is that the pointgroup is > P222. > > The next peak down the list is only 0.13 for one and 0.17 for the > other pointgroup, which only borders on significance.. > But this doesnt really prove anything - for example, if there is a > flexible linker the 2 domains of each molecule may be in different > relative orientations . Do you have any MR search model for the 2 > domains? I would search with them and see what they predict - on the > whole self rotation functions are most comprehensible AFTER the > structure is solved! > > Eleanor > > > On 18 November 2013 09:58, Monica Mittal wrote: >> Dear CCp4 users, >> May anyone help me in interpreting >> the self-rotation function from molrep. Data can be indexed,scaled >> equally well in P21 and P222. This protein has two domain linked by a >> long flexible linker and get cleaved during crystallization. After >> crystallizing it in many condition, i believed that i found new >> condition where it may be full length. May anyone please suggest me >> by looking at the self-rotation function, how many molecule exist in ASU. >> Matthews coefficient suggest that there would be 2 copy of full >> length protein or four of truncated protein in P21 space group. For >> your interpretation, please find attached images of rotation function >> around K=180 Molrep self rotation peaks are >> >> P21 space group >> >> theta phi chi P(i)/P(0)| >> +--+ >> | 1 0.000.000.001.00 | >> | 290.00 -0.00 180.000.79 | >> | 335.78 -0.00 180.000.17 | >> | 490.00 -170.05 180.000.17 | >> | 558.71 180.00 180.000.14 | >> | 6 108.34 180.00 180.000.14 | >> | 7 117.39 180.00 180.000.13 | >> | 890.00 90.00 108.540.13 | >> | 990.00 -90.00 108.540.13 | >> | 10 144.50 -0.00 180.000.13 | >> | 1137.57 25.59 179.980.12 | >> | 12 148.100.00 180.000.12 | >> | 13 121.736.36 179.620.11 | >> | 1463.31 -42.27 180.000.11 | >> | 1590.00 90.00 162.290.11 | >> | 1690.00 -90.00 162.290.11 | >> | 1771.12 136.88 180.000.10 | >> | 1899.17 -180.00 180.000.10 | >> | 19 144.80 -161.87 180.000.10 | >> | 2090.00 -138.24 180.000.10 | >> | 2182.27 -76.45 180.000.10 | >> | 2290.00 90.00 115.940.10 | >> | 2390.
Re: [ccp4bb] SELF-ROTATION FUNCTION FROM MOLREP
Dear CCP4 Users, In Phenix.xtriage and phaser, the analyses of the Patterson function reveals a significant off-origin peak that is 23.25 % of the origin peak, indicating pseudo translational symmetry at frac. cord. vector 0.0000.5000.022 . It did not indicate any twinng. Data is good with resolution upto 2.8A. The cell dimension in P21 SG is 57.877, 63.321, 108.028, 90, 89.987, 90 and in P222 SG is 57.805, 63.266, 108.053, 90, 90, 90. We can say cell dimension align well in in P21 and P222 SG. For MR template, about 75% of domain1, we have solved in our lab and remaining 25% is available from pdb with 30% sequence identity. It is a transcription factor with ligand bindng domain and DNA binding domain. I tried finding MR solution but does not gave satisfaction result. The Rwork and Rfree stalls around 47% and 53% respectively. Is there any possiblity to guess the no of molecules present in ASU from self-rotation function? If we can then we will be sure of whether it is full length of truncated one. Thank you Monica On 11/18/13, Eleanor Dodson wrote: > First Q - how good is your data - is there no possibility of twinning > or any other distraction? > > Second Q - To compare those results properly we need to know how the > P2 and the P222 cell align - are the cell dimensions more or less the > same? > > But the 2 plots you attach (and the list above) show both very strong > 222 symmetry so the most likely assumption is that the pointgroup is > P222. > > The next peak down the list is only 0.13 for one and 0.17 for the > other pointgroup, which only borders on significance.. > But this doesnt really prove anything - for example, if there is a > flexible linker the 2 domains of each molecule may be in different > relative orientations . Do you have any MR search model for the 2 > domains? I would search with them and see what they predict - on the > whole self rotation functions are most comprehensible AFTER the > structure is solved! > > Eleanor > > > On 18 November 2013 09:58, Monica Mittal wrote: >> Dear CCp4 users, >> May anyone help me in interpreting the >> self-rotation function from molrep. Data can be indexed,scaled equally >> well in P21 and P222. This protein has two domain linked by a long >> flexible linker and get cleaved during crystallization. After >> crystallizing it in many condition, i believed that i found new >> condition where it may be full length. May anyone please suggest me by >> looking at the self-rotation function, how many molecule exist in ASU. >> Matthews coefficient suggest that there would be 2 copy of full >> length protein or four of truncated protein in P21 space group. For >> your interpretation, please find attached images of rotation function >> around K=180 >> Molrep self rotation peaks are >> >> P21 space group >> >> theta phi chi P(i)/P(0)| >> +--+ >> | 1 0.000.000.001.00 | >> | 290.00 -0.00 180.000.79 | >> | 335.78 -0.00 180.000.17 | >> | 490.00 -170.05 180.000.17 | >> | 558.71 180.00 180.000.14 | >> | 6 108.34 180.00 180.000.14 | >> | 7 117.39 180.00 180.000.13 | >> | 890.00 90.00 108.540.13 | >> | 990.00 -90.00 108.540.13 | >> | 10 144.50 -0.00 180.000.13 | >> | 1137.57 25.59 179.980.12 | >> | 12 148.100.00 180.000.12 | >> | 13 121.736.36 179.620.11 | >> | 1463.31 -42.27 180.000.11 | >> | 1590.00 90.00 162.290.11 | >> | 1690.00 -90.00 162.290.11 | >> | 1771.12 136.88 180.000.10 | >> | 1899.17 -180.00 180.000.10 | >> | 19 144.80 -161.87 180.000.10 | >> | 2090.00 -138.24 180.000.10 | >> | 2182.27 -76.45 180.000.10 | >> | 2290.00 90.00 115.940.10 | >> | 2390.00 -90.00 115.940.10 | >> | 24 159.16 27.07 180.000.10 | >> | 2595.08 -35.92 179.840.10 | >> | 26 113.86 -139.44 179.540.10 | >> | 2790.23 -0.00 89.320.10 | >> | 2820.18 -156.63 179.980.10 | >> | 29 116.90 -40.40 179.500.10 | >> | 3063.12 139.60 179.500.10 >> >> >> P222 space group >> >> theta phi chi P(i)/P(0)| >> +--+ >> | 1 0.000.000.001.00 | >> | 290.00 -21.41 180.000.13 | >> | 3 125.320.00 180.000.13 | >> | 4 151.18 -90.00 180.000.12 | >> | 590.00 -180.00 90.000.12 | >> | 6 141.32 26.82 180.000.12 | >> | 790.00 -42.59 180.000.11 | >> | 8 127.22 -25.21 180.000.11 | >> | 937.04 -14.48 180.00
Re: [ccp4bb] NCS edits in COOT
Dear Felix, under "Draw" you can find the option "NCS Ghost Control ...". You can change the master chain there. Good luck! Karsten > > I have a very large complex of proteins and I would like > to use COOT to apply NCS edits in the case where the > "master copy" is not chain A of my complex but any given > chain. > The script that I currently use (example only, actual > number of molecules is much larger) > > (copy-residue-range-from-ncs-master-to-chains 0 "A" 1 500 (list "B" > "C" "D" "E")) > > works only for A but for this I need to temporarily rename > molecules, making any molecule I wish to be "master" > also to be "A". > It is O.K. to do this renaming once or twice, but not > convenient if the extensive rebuilding of the complex is > considered. > > Q1. Is there currently a possibility to use a different > chain as the master for the NCS edits in COOT? > Q2. If so, could someone please let me know how? > Q3. If not, would it be possible to program this into > Coot for the future for complicated cases? > Q4. Is there another option, not COOT? > > > > > > > > > > > Dr Felix Frolow > Professor of Structural Biology andBiotechnology, > Department of MolecularMicrobiology and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica F, co-editor > > e-mail: mbfro...@post.tau.ac.il > Tel: ++972-3640-8723 > Fax: ++972-3640-9407 > Cellular: 0547 459 608 > > --- Karsten Niefind, PhD University of Cologne Department of Chemistry Institute of Biochemistry Otto-Fischer-Str. 12-14 D-50674 Cologne Tel.: +49 221 470 6444 Fax: +49 221 470 3244
[ccp4bb] NCS edits in COOT
I have a very large complex of proteins and I would like to use COOT to apply NCS edits in the case where the “master copy” is not chain A of my complex but any given chain. The script that I currently use (example only, actual number of molecules is much larger) (copy-residue-range-from-ncs-master-to-chains 0 "A" 1 500 (list "B" "C" "D" "E")) works only for A but for this I need to temporarily rename molecules, making any molecule I wish to be "master" also to be "A". It is O.K. to do this renaming once or twice, but not convenient if the extensive rebuilding of the complex is considered. Q1. Is there currently a possibility to use a different chain as the master for the NCS edits in COOT? Q2. If so, could someone please let me know how? Q3. If not, would it be possible to program this into Coot for the future for complicated cases? Q4. Is there another option, not COOT? Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] Weird MR result
Hmm - why should a translational peak not be along the 40 axis? Anyway othercell shows this Conversion of cell 40, 32, 101, 90, 101, 90 can give Laue groups C m m m 40.0 198.3 32.0 90.0 90.0 89.60.42 [h,h+2l,-k] Possible spacegroups: or C 1 2/m 1 40.0 198.3 32.0 90.0 90.0 89.60.42 [h,h+2l,-k] or C 1 2/m 1 198.3 40.0 32.0 90.0 90.0 90.40.42 [-h-2l,h,-k] or P 1 2/m 1 40.0 32.0 101.3 90.0 101.8 90.00.84 [-h,-k,h+l] That is so close to your input cell that twinning is a very likely option. What does thedata processing suggest - look at pointless or Xtriage or something Eleanor On 15 November 2013 18:18, Niu Tou wrote: > It may be helpful to add some information during index. HKL2000 could find > four reasonable solutions: > 40, 32, 101, 90, 101, 90 for P1 and P2 > 200, 40, 32, 90, 90, 90 for C2 and C222 > > It looks very strange to me since these two unit cells look differently, but > during refinement the predicated spots are identical, and they produced > similar quality data--at least from those output > parameters. > > All solutions (including P21, C2221) have the 95% off origin peak and > several minor ones. The 95% peak is at (0.5 0 0) on the 40 line, so if cut > it into half, that dimension will be too small (20 only). HKL2000 also did > not give any solution with one dimension as 20. > > Maybe I did not get a right index yet, I wonder any expert can tell > something from these information? > > > On Fri, Nov 15, 2013 at 6:41 AM, Melanie Vollmar > wrote: >> >> Dear Niu, >> >> I had an interesting pseudo-translation case recently where my off-origin >> peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, >> c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable >> and the model could be built. I had background density which I thought of as >> water. I got suspicious when I identified density for a helix which was near >> my build main chain but could not be joined and built or be accounted for by >> looking at symmetry mates. Moreover I got stuck in refinement with R/Rfree >> 25/30%. I could identify which part of the protein caused me the trouble on >> crystal packing and the appearance of the off-origin peak. In my case it was >> the C terminus. So I used a new construct with swapped purification tag (N >> to C terminus). This altered the peptide sequence for the C terminus and >> allowed the protein to pack nicely into I222. This turned my off-origin peak >> into a true symmetry operator. >> >> I also had reasonable processing and phasing results for P2 and C2. >> >> So besides the strength of your off-origin peak it may be off some use to >> look at the location. >> >> HTH >> >> Melanie >> >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou >> [niutou2...@gmail.com] >> Sent: 14 November 2013 23:58 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Weird MR result >> >> Dear Phil, >> >> I used PHASER to do the task. I have double checked and both files have >> the same prefix, so they are from the same output. I have also checked the >> headers again, they have the same spacegroup. Actually I was trying to >> search for two different molecules but only one was found. The spacegeoup is >> P2 and I am quite sure it is not P21 from system absence. >> >> One possibility is that the space group was wrong, since there is a 95% >> off origin peak. There are several choices from data processing, P1, P2, C2 >> C222, all have this large off origin peak. I wonder if this 95% peak can >> tell some information? >> >> It will not surprise me if this result is incorrect, however how could >> these regular density be? >> >> Best, >> Niu >> >> >> On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey >> wrote: >>> >>> Hello Niu, >>> >>> 1. We need extra information. What program did you use ? What's the >>> similarity (e.g. % identity) of your model. What's your space group ? Did >>> you try ALL the space groups in your point group in ALL the permutations >>> (e.g. in primitive orthorhombic there are 8 possibilities). >>> >>> 1a. My best guess on limited info is that you've got a partial solution >>> in the wrong space group with only part of the molecules at their correct >>> position. >>> >>> 2. I recently had a very unusual case where I could solve a structure in >>> EITHER P41212 or P43212 with similar statistics, but that I would see >>> interpenetrating electron density for a second, partial occupancy molecule >>> no matter which of these space groups I tried (and it showed this when I >>> expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, >>> in retrospect, but we obtained a more friendly crystal form. I hope you >>> don't have something like that, but it's possible. >>> >>> Phil Jeffrey >>> Princeton >>> >>> >>> On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know ho
Re: [ccp4bb] translational pseudo symmetry
I guess you have checked that P43212 is a better match than P41212? (And that you are running REFMAC against an mtz file with the same symmetry as the input PDB - you may need to change the SG in the mtz header by hand. mtzutils hklin P41212.mtz hklout P43212.mtz symm P43212 end Or vice versa.. Sorry - THIS IS CRAZY but there you are.. Re the pseudo translation -Randy summs up the situation very clearly. I would build my model by hand actually but I am sure PHASER does itwell too! Something I dont understand but maybe it is to do with your patterson sampling. Peak 3 is a consequence of Pk 1 and Pk2 - Pk 5 is the consequence of Pk 1 and Pk4 but the peak heights dont exactly fit.. Eleanor On 18 November 2013 10:19, Randy Read wrote: > Dear Dan, > > First, you don't want to reprocess in the smaller cell. What xtriage is > saying is that, if *and only if* the translation detected in the Patterson > map were an exact crystallographic translation, then you would get the > smaller cell. However, in order for that to be a plausible hypothesis, the > Patterson peaks would have to be near to 100% of the origin peak. > > You actually seem to have a very interesting case, where the Patterson peaks > are related by multiples of approximately the same translation. If you take > a translation of 1/2,1/2,1/6 and multiply it by 1, 2 and 3, you get > something close to the three biggest peaks in your Patterson (taking account > of lattice translations), and these are related by the Patterson inversion > centre to what you get if you multiply by 4 and 5. So the six molecules > should be related to each other by something close to a repeated translation > of 1/2,1/2,1/6. (You should check this in the solution that you already > have.) If this were exact, you would have a smaller cell, but it's not > exact, and one way in which it is not exact is that the translations along z > are not exactly multiples of 1/6. > > This is reminiscent of a structure that we recently collaborated with > Mariusz Jaskolski and Zbyszek Dauter to solve (paper accepted for > publication in Acta D). In that case, there are seven translations of > approximately 0,0,1/7. The difficulty with cases like this is figuring out > how to break the exact symmetry. Any solution that has approximately the > right translations will basically fit the data, but you need to find the > right combination of deviations from the exact symmetry to get an optimal > answer. If you get the wrong deviations from exact symmetry, the refinement > will stall, and this may be the problem that you're facing. > > You can deal with problems like this in Phaser by using the TNCS NMOL 6 > command (to say that there are 6 copies related by repeated applications of > the same translation). You should tell Phaser to use the 1/2,1/2,0.174 > vector (TNCS TRA VECTOR 0.5 0.5 0.174), and hopefully this will break the > symmetry in a way that subsequent rigid-body refinement can deal with. I'm > happy to give you more advice on this, off-line, because this kind of case > isn't something that we've figured out how to deal with automatically yet. > The optimal approach probably involves getting a deeper understanding of > commensurate modulation, which is another way of thinking about > pseudo-translations. > > Best wishes, > > Randy Read > > On 18 Nov 2013, at 09:19, #CHEN DAN# wrote: > > Dear experts, > > I am working on one dataset (2.5A) which was processed using space group > P43212 ( 107.9, 107.9, 313.7; 90, 90, 90). > After running MR with 6 molecules in ASU and one round of refmac, the R > factors are high (38%/45%). > I ran phenix.xtriage and found that translational pseudo symmetry is likely > present. It suggested that the space group is I4122 with the unit cell about > 1/3 smaller (I paste the patterson analyses below). > I tried to reprocess the data to get the suggested space group and unit cell > using HKL2000. But the index always gives a long c axis about 313A. > Could you provide any suggestions on how to proceed? > > Patterson analyses > -- > > Largest Patterson peak with length larger than 15 Angstrom > > Frac. coord.:0.5000.5000.174 > Distance to origin : 93.757 > Height (origin=100) : 55.763 > p_value(height) :3.018e-05 > > >The reported p_value has the following meaning: > The probability that a peak of the specified height > or larger is found in a Patterson function of a > macro molecule that does not have any translational > pseudo symmetry is equal to 3.018e-05. > p_values smaller than 0.05 might indicate > weak translational pseudo symmetry, or the self vector of > a large anomalous scatterer such as Hg, whereas values > smaller than 1e-3 are a very strong indication for > the presence of translational pseudo symmetry. > > The full list of Patterson peaks is: > > x y zheight p-value(height) > ( 0.500, 0.500, 0.17
Re: [ccp4bb] SELF-ROTATION FUNCTION FROM MOLREP
First Q - how good is your data - is there no possibility of twinning or any other distraction? Second Q - To compare those results properly we need to know how the P2 and the P222 cell align - are the cell dimensions more or less the same? But the 2 plots you attach (and the list above) show both very strong 222 symmetry so the most likely assumption is that the pointgroup is P222. The next peak down the list is only 0.13 for one and 0.17 for the other pointgroup, which only borders on significance.. But this doesnt really prove anything - for example, if there is a flexible linker the 2 domains of each molecule may be in different relative orientations . Do you have any MR search model for the 2 domains? I would search with them and see what they predict - on the whole self rotation functions are most comprehensible AFTER the structure is solved! Eleanor On 18 November 2013 09:58, Monica Mittal wrote: > Dear CCp4 users, > May anyone help me in interpreting the > self-rotation function from molrep. Data can be indexed,scaled equally > well in P21 and P222. This protein has two domain linked by a long > flexible linker and get cleaved during crystallization. After > crystallizing it in many condition, i believed that i found new > condition where it may be full length. May anyone please suggest me by > looking at the self-rotation function, how many molecule exist in ASU. > Matthews coefficient suggest that there would be 2 copy of full > length protein or four of truncated protein in P21 space group. For > your interpretation, please find attached images of rotation function > around K=180 > Molrep self rotation peaks are > > P21 space group > > theta phi chi P(i)/P(0)| > +--+ > | 1 0.000.000.001.00 | > | 290.00 -0.00 180.000.79 | > | 335.78 -0.00 180.000.17 | > | 490.00 -170.05 180.000.17 | > | 558.71 180.00 180.000.14 | > | 6 108.34 180.00 180.000.14 | > | 7 117.39 180.00 180.000.13 | > | 890.00 90.00 108.540.13 | > | 990.00 -90.00 108.540.13 | > | 10 144.50 -0.00 180.000.13 | > | 1137.57 25.59 179.980.12 | > | 12 148.100.00 180.000.12 | > | 13 121.736.36 179.620.11 | > | 1463.31 -42.27 180.000.11 | > | 1590.00 90.00 162.290.11 | > | 1690.00 -90.00 162.290.11 | > | 1771.12 136.88 180.000.10 | > | 1899.17 -180.00 180.000.10 | > | 19 144.80 -161.87 180.000.10 | > | 2090.00 -138.24 180.000.10 | > | 2182.27 -76.45 180.000.10 | > | 2290.00 90.00 115.940.10 | > | 2390.00 -90.00 115.940.10 | > | 24 159.16 27.07 180.000.10 | > | 2595.08 -35.92 179.840.10 | > | 26 113.86 -139.44 179.540.10 | > | 2790.23 -0.00 89.320.10 | > | 2820.18 -156.63 179.980.10 | > | 29 116.90 -40.40 179.500.10 | > | 3063.12 139.60 179.500.10 > > > P222 space group > > theta phi chi P(i)/P(0)| > +--+ > | 1 0.000.000.001.00 | > | 290.00 -21.41 180.000.13 | > | 3 125.320.00 180.000.13 | > | 4 151.18 -90.00 180.000.12 | > | 590.00 -180.00 90.000.12 | > | 6 141.32 26.82 180.000.12 | > | 790.00 -42.59 180.000.11 | > | 8 127.22 -25.21 180.000.11 | > | 937.04 -14.48 180.000.11 | > | 1059.17 -129.14 180.000.10 | > | 1156.66 -174.09 180.000.09 | > | 1240.85 144.82 180.000.09 | > | 1354.16 -167.88 180.000.09 | > | 14 109.29 -61.09 180.000.09 | > | 15 123.12 -84.90 180.000.09 | > | 1664.66 -93.79 180.000.09 | > | 17 113.09 108.59 179.890.09 | > | 1893.84 37.37 179.940.08 | > | 1990.00 -33.41 180.000.08 | > | 20 131.95 90.00 90.750.08 | > | 2153.78 -144.59 180.000.08 | > | 2249.15 -43.11 180.000.08 | > | 2362.98 -56.60 180.000.08 | > | 2461.97 138.06 179.910.08 | > | 2596.77 59.47 179.900.08 | > | 26 118.74 40.91 179.850.07 | > | 27 100.14 57.97 179.860.07 | > | 2859.74 -139.98 180.000.07 | > | 2958.97 -141.14 180.000.07 | > | 30 103.38 59.92 179.810.07 > > Many Thanks in advance for your kind help. > THANK YOU
Re: [ccp4bb] I want to dock/align an EM envelope (MRC) into a DM averaging and/or solvent envelope (MSK).
There are ways - the EM map is your model equiv to a PDB file and you need to generate a set of "structure factors" from your map - the EM density is put into a large box and transformed by a program such as sfall. . Is that possible for you? There are problems of scaling etc etc.. On 15 November 2013 00:58, Francis Reyes wrote: > Is there a single tool or suite of tools that addresses this? Or a CCP4 > workflow if need be. > > > Thanks! > > F > > > > - > Francis E. Reyes PhD > 215 UCB > University of Colorado at Boulder
Re: [ccp4bb] [CCP4] Converting ShelX .phs to mtz
SHELX only gives phases for the I+ (or actually I suppose Imean) so you may not expect to get 100% completeness. Geed your sca file into the scalepack2mtz task - that gives you a file with h k l I+ SigI+ I- SigI- Maybe automatically that goes into truncate to generate h k l Fmean SigFmean F+ SigF+ F- SigF- Imean I+ SigI+ I- SigI- and FreeRlag to add FreeR flags.. (look at the completeness of that file as well as the intensity statistic plots) And then combine that one with the SHELX PHI FOM Is that OK? Eleanor On 14 November 2013 23:14, Yarrow Madrona wrote: > Hi Yury, > > Your idea seemed to work well, however I now have 50% completeness in phi > and 100% completeness in Intensities. > > I am not sure where I am going wrong. > > > H K L IMEAN FOM PHI SIGIMEAN >> Hi Yarrow, >> >> You may consider producing mtz file from your original .sca or .hkl file >> first. Then take the .mtz file you have created from a .phs file and merge >> the two using CAD in CCP4. I assume you need only phase information from >> you .phs file, so select only two sets of parameters - FOM and PHIB - from >> there and take the rest from the first file. The result will be a complete >> merge.mtz with all original data plus phase information. This will assure >> you do not loose anything on the way. >> >> Good luck, >> >> >> Yury >> >> >> >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yarrow >> Madrona [amadr...@uci.edu] >> Sent: Thursday, November 14, 2013 3:43 PM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] [CCP4] Converting ShelX .phs to mtz >> >> Hello CCP4 users, >> >> I seem to be loosing data (50%) when converting shelX .phs reflelection >> file to mtz format using F2MTZ. I think it has something to do with >> loosing my anamolous data. Is it possible to merge the anamolous data >> before conversion or to tell F2MTZ to include it. >> >> These are my labels: >> >> H K L I FOM PHI SIGI >> >> Thank you >> >> Yarrow Madrona >> >> >> >> > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697
Re: [ccp4bb] translational pseudo symmetry
Dear Dan, First, you don't want to reprocess in the smaller cell. What xtriage is saying is that, if *and only if* the translation detected in the Patterson map were an exact crystallographic translation, then you would get the smaller cell. However, in order for that to be a plausible hypothesis, the Patterson peaks would have to be near to 100% of the origin peak. You actually seem to have a very interesting case, where the Patterson peaks are related by multiples of approximately the same translation. If you take a translation of 1/2,1/2,1/6 and multiply it by 1, 2 and 3, you get something close to the three biggest peaks in your Patterson (taking account of lattice translations), and these are related by the Patterson inversion centre to what you get if you multiply by 4 and 5. So the six molecules should be related to each other by something close to a repeated translation of 1/2,1/2,1/6. (You should check this in the solution that you already have.) If this were exact, you would have a smaller cell, but it's not exact, and one way in which it is not exact is that the translations along z are not exactly multiples of 1/6. This is reminiscent of a structure that we recently collaborated with Mariusz Jaskolski and Zbyszek Dauter to solve (paper accepted for publication in Acta D). In that case, there are seven translations of approximately 0,0,1/7. The difficulty with cases like this is figuring out how to break the exact symmetry. Any solution that has approximately the right translations will basically fit the data, but you need to find the right combination of deviations from the exact symmetry to get an optimal answer. If you get the wrong deviations from exact symmetry, the refinement will stall, and this may be the problem that you're facing. You can deal with problems like this in Phaser by using the TNCS NMOL 6 command (to say that there are 6 copies related by repeated applications of the same translation). You should tell Phaser to use the 1/2,1/2,0.174 vector (TNCS TRA VECTOR 0.5 0.5 0.174), and hopefully this will break the symmetry in a way that subsequent rigid-body refinement can deal with. I'm happy to give you more advice on this, off-line, because this kind of case isn't something that we've figured out how to deal with automatically yet. The optimal approach probably involves getting a deeper understanding of commensurate modulation, which is another way of thinking about pseudo-translations. Best wishes, Randy Read On 18 Nov 2013, at 09:19, #CHEN DAN# wrote: > Dear experts, > > I am working on one dataset (2.5A) which was processed using space group > P43212 ( 107.9, 107.9, 313.7; 90, 90, 90). > After running MR with 6 molecules in ASU and one round of refmac, the R > factors are high (38%/45%). > I ran phenix.xtriage and found that translational pseudo symmetry is likely > present. It suggested that the space group is I4122 with the unit cell about > 1/3 smaller (I paste the patterson analyses below). > I tried to reprocess the data to get the suggested space group and unit cell > using HKL2000. But the index always gives a long c axis about 313A. > Could you provide any suggestions on how to proceed? > > Patterson analyses > -- > > Largest Patterson peak with length larger than 15 Angstrom > > Frac. coord.:0.5000.5000.174 > Distance to origin : 93.757 > Height (origin=100) : 55.763 > p_value(height) :3.018e-05 > > >The reported p_value has the following meaning: > The probability that a peak of the specified height > or larger is found in a Patterson function of a > macro molecule that does not have any translational > pseudo symmetry is equal to 3.018e-05. > p_values smaller than 0.05 might indicate > weak translational pseudo symmetry, or the self vector of > a large anomalous scatterer such as Hg, whereas values > smaller than 1e-3 are a very strong indication for > the presence of translational pseudo symmetry. > > The full list of Patterson peaks is: > > x y zheight p-value(height) > ( 0.500, 0.500, 0.174 ) : 55.763 (3.018e-05) > ( 0.500, 0.500, 0.500 ) : 51.209 (5.796e-05) > ( 0.000, 0.000, 0.326 ) : 32.915 (8.699e-04) > ( 0.000, 0.000, 0.348 ) : 18.765 (1.266e-02) > ( 0.500, 0.500, 0.151 ) : 11.396 (9.756e-02) > > If the observed pseudo translationals are crystallographic > the following spacegroups and unit cells are possible: > > space groupoperator unit cell of reference setting > I 41 2 2 (a+1/4,b+1/4,3*c) x+1/2, y+1/2, z+1/6 (107.94, 107.94, 104.58, > 90.00, 90.00, 90.00) > > > Thanks, > Dan -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road
[ccp4bb] translational pseudo symmetry
Dear experts, I am working on one dataset (2.5A) which was processed using space group P43212 ( 107.9, 107.9, 313.7; 90, 90, 90). After running MR with 6 molecules in ASU and one round of refmac, the R factors are high (38%/45%). I ran phenix.xtriage and found that translational pseudo symmetry is likely present. It suggested that the space group is I4122 with the unit cell about 1/3 smaller (I paste the patterson analyses below). I tried to reprocess the data to get the suggested space group and unit cell using HKL2000. But the index always gives a long c axis about 313A. Could you provide any suggestions on how to proceed? Patterson analyses -- Largest Patterson peak with length larger than 15 Angstrom Frac. coord.:0.5000.5000.174 Distance to origin : 93.757 Height (origin=100) : 55.763 p_value(height) :3.018e-05 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 3.018e-05. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. The full list of Patterson peaks is: x y zheight p-value(height) ( 0.500, 0.500, 0.174 ) : 55.763 (3.018e-05) ( 0.500, 0.500, 0.500 ) : 51.209 (5.796e-05) ( 0.000, 0.000, 0.326 ) : 32.915 (8.699e-04) ( 0.000, 0.000, 0.348 ) : 18.765 (1.266e-02) ( 0.500, 0.500, 0.151 ) : 11.396 (9.756e-02) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space groupoperator unit cell of reference setting I 41 2 2 (a+1/4,b+1/4,3*c) x+1/2, y+1/2, z+1/6 (107.94, 107.94, 104.58, 90.00, 90.00, 90.00) Thanks, Dan
[ccp4bb] CCP4 study weekend 2014 on Complementary Techniques - Early bird registration closes this Sunday!!!!!
A reminder about the CCP4 Study weekend 4-5 January 2014 on Complementary Techniques. Please note: Deadline for early bird registration is 24th November (this Sunday). After this date the registration fee increases and there will be no student bursaries available. Up-to-date details of the meeting programme can be found at this link: http://www.cse.scitech.ac.uk/events/CCP4_2014/programme.html For registration, please follow the link: https://eventbooking.stfc.ac.uk/login?EVENT=147 What techniques can be combined with crystallographic analysis? Of all deposited structures in the PDB, more than half are oligomeric, and three quarters have a ligand bound. In-solution methods like SAXS or biophysical techniques allow us to validate the information on the molecular assembly. Biophysical techniques are also essential to probe ligands and co-factors. We address how to make ligand complexes with novel methods to mount and manipulate crystals. A session on drug design gives the perspective and discusses additional techniques such as NMR. Simulations and NMR also address the dynamic nature of macromolecules. EM techniques can be used to address macromolecular complexes of changing composition and go full circle with the X-ray analysis. You will learn how complementary methods help in structure determination and analysis, leading to a better understanding of the bio-macromolecules we study. The organisers. Ivo Tews, University of Southampton Jon Cooper, UCL. -- Scanned by iCritical.
[ccp4bb] sCCP4 study weekend 2014 on Complementary Techniques - Early bird registration closes this Friday!!!!!
A reminder about the CCP4 Study weekend 4-5 January 2014 on Complementary Techniques. Please note: Deadline for early bird registration is 24th November (this Friday). After this date the registration fee increases and there will be no student bursaries available. Up-to-date details of the meeting programme can be found at this link: http://www.cse.scitech.ac.uk/events/CCP4_2014/programme.html For registration, please follow the link: https://eventbooking.stfc.ac.uk/login?EVENT=147 What techniques can be combined with crystallographic analysis? Of all deposited structures in the PDB, more than half are oligomeric, and three quarters have a ligand bound. In-solution methods like SAXS or biophysical techniques allow us to validate the information on the molecular assembly. Biophysical techniques are also essential to probe ligands and co-factors. We address how to make ligand complexes with novel methods to mount and manipulate crystals. A session on drug design gives the perspective and discusses additional techniques such as NMR. Simulations and NMR also address the dynamic nature of macromolecules. EM techniques can be used to address macromolecular complexes of changing composition and go full circle with the X-ray analysis. You will learn how complementary methods help in structure determination and analysis, leading to a better understanding of the bio-macromolecules we study. The organisers. Ivo Tews, University of Southampton Jon Cooper, UCL. -- Scanned by iCritical.
